http://imagejdocu.tudor.lu/ 2013-05-22T00:52:19+02:00 http://imagejdocu.tudor.lu/ http://imagejdocu.tudor.lu/lib/images/favicon.ico text/html 2013-05-17T16:39:03+02:00 mutterer http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start&rev=1368801543&do=diff This plugin allows counting objects in 3D, and getting some measurements about each object found. Author Fabrice P. Cordelières, Institut Curie, Orsay (France). Fabrice.Cordelieres at curie.u-psud.fr Features This plugin: * counts the number of 3D objects in a stack. * quantifies for each found object the following parameters: * Integrated density; * Mean of the gray values; * Standard deviation of the gray values; * Minimum gray value; * Maximum gray value; * Median… text/html 2013-05-17T13:54:12+02:00 aatorrano http://imagejdocu.tudor.lu/doku.php?id=macro:particle_in_cell-3d&rev=1368791652&do=diff Particle_in_Cell-3D is an ImageJ Macro designed to quantify the uptake of macro- and nanoparticles by cells. Input Routines 1, 2 and 3: * Confocal fluorescence image stack of a single cell with stained plasma membrane * Respective image stack of nanoparticles text/html 2013-05-16T08:41:20+02:00 mutterer http://imagejdocu.tudor.lu/doku.php?id=faq:technical:are_there_performance_statistics_to_compare_against_my_system&rev=1368686480&do=diff What is ImageJ's typical performance on various system configurations, and how does my machine compare to them? ImageJ has a Benchmark utility you can run to evaluate your system's performance. * Start up a fresh ImageJ. * Choose File > New Text Window from the menu. * Paste in the benchmark test macro (in the blue box below, thanks to Gabriel Landini for providing it). * Choose Macros > Run Macro from the menu to execute the benchmark. * Compare your results against the table below… text/html 2013-05-03T13:13:33+02:00 gadeamm http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:neuronpersistentj:start&rev=1367579613&do=diff Introduction This free code is an ImageJ plugin that allows one to detect the neuronal structure from image. This plugin, is a joint work between the team "Structural Synaptic Plasticity" of The Biomedical Research Centre of La Rioja (CIBIR) and "Programming and Symbolic Computation Team” of University of La Rioja. text/html 2013-04-29T22:00:53+02:00 gilbertbigras http://imagejdocu.tudor.lu/doku.php?id=plugin:color:colour_deconvolution:optimizing_selection_of_unitary_optical_density_vectors:start&rev=1367265653&do=diff INTRODUCTION This software was designed to ease the determination of unitary optical density vectors used in the color decovolution plugin written by Gabriel Landini <http://www.dentistry.bham.ac.uk/landinig/software/software.html> and based on the original publication by Ruifrok and Johnston:Quantification of histochemical staining by color deconvolution. The major idea of this imageJ plugin relies on the fact that 3D optical density unitary vectors (which are the core of the colour deconvolu… text/html 2013-04-19T18:35:28+02:00 jphil http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:micropatterned_single_cell_sorting_mscs_:start&rev=1366389328&do=diff use this plugin to sort micropatterned single cell images from high-throughput experiments. Jean-Philippe Grossier jp.grossier at gmail dot com handle 96well format images process multiple experiments/plates can sort different micropatterns according to their size text/html 2013-04-12T23:14:19+02:00 tferreira http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:asa:start&rev=1365801259&do=diff For the Fiji plugin, visit the Fiji website. For analysis of traced arbors have a look at Simple Neurite Tracer. Introduction [Sholl mask] This ImageJ plugin performs 2D and 3D Sholl analysis on grayscale images of single neurons. Sholl is a popular technique used by neuroanatomists to describe neuronal arbors. The major advantages of this plugin over other implementations are: text/html 2013-04-12T12:21:12+02:00 nshimirimana http://imagejdocu.tudor.lu/doku.php?id=plugin:start&rev=1365762072&do=diff Descriptions and downloads for ImageJ plugins stored here. There are many more plugins in the ImageJ website. Acquisition * ImageJVI Aligning * Align_4 * Align_RGB_planes * Align_Slice * bUnwarpJ: consistent and elastic registration * Image Stabilizer text/html 2013-04-12T12:13:43+02:00 nshimirimana http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:radial_thickness_measure:start&rev=1365761623&do=diff Measure the radial distribution of the cross section thickness within the region of interest(circle or a circular sector) Robert Nshimirimana Line selection measurement This program will measure the radial distribution of the cross section thickness within the region of interest(circle or a circular sector)defined by the radius and the angular range. The thickness is calculated along the line of each step angle from the center of the region of interest. The required inputs are: radius and… text/html 2013-04-10T18:06:26+02:00 rkd8 http://imagejdocu.tudor.lu/doku.php?id=macro:mitpophagy_mitochondrial_morphology_content_lc3_colocalization_macro&rev=1365609986&do=diff Mitophagy Introduction Microtubule associated protein light chain 3(LC3) is a ubiquitin-like protein that binds to autophagosomes (AVs). Cellular biologists transfect mammalian cells with GFP tagged LC3 to track and follow the fate of AVs in the cell and to measure autophagic flux. Also, GFP-LC3 puncta that colocalize with mitochondria is a way to measure the initiation of mitochondrial autophagy, the catabolic process by which mitochondria are targeted for lysosomal degradation. text/html 2013-04-10T18:03:49+02:00 rkd8 http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:mitochondrial_morphology_macro_plug-in:start&rev=1365609829&do=diff Mito-Morphology Macro Introduction This macro allows you to measure mitochondrial interconnectivity and elongation from epifluorescence micrographs of cells immunostained for mitochondria or transiently expressing mitochondrially targeted GFP. This macro was designed by Ruben K. Dagda while working at the Chu lab at the University of Pittsburgh (2010). This macro only works on the old version of Image J, and for versions 1.44 and 1.46. text/html 2013-04-10T10:40:46+02:00 mutterer http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start&rev=1365583246&do=diff This plugin achieves easy creation of image figures for publications, reports, projects. Authors Jerome Mutterer (CNRS) and Edda Zinck (HTW). Contact: mutterer[at]ibmp.fr Credits * CNRS, IBMP, Strasbourg, France * HTW, Berlin, Germany * Carl Zeiss Microscopy supports this project as part of the Open Application Development initiative.